Global inference of disease-causing single nucleotide variants from exome sequencing data

[1]  Rui Jiang,et al.  dbWGFP: a database and web server of human whole-genome single nucleotide variants and their functional predictions , 2016, Database J. Biol. Databases Curation.

[2]  J. Buxbaum,et al.  A SPECTRAL APPROACH INTEGRATING FUNCTIONAL GENOMIC ANNOTATIONS FOR CODING AND NONCODING VARIANTS , 2015, Nature Genetics.

[3]  Naomichi Matsumoto,et al.  Phenotypic spectrum of GNAO1 variants: epileptic encephalopathy to involuntary movements with severe developmental delay , 2015, European Journal of Human Genetics.

[4]  Rui Jiang,et al.  Prioritization Of Nonsynonymous Single Nucleotide Variants For Exome Sequencing Studies Via Integrative Learning On Multiple Genomic Data , 2015, Scientific Reports.

[5]  Yuval Itan,et al.  Can the impact of human genetic variations be predicted? , 2015, Proceedings of the National Academy of Sciences.

[6]  O. Troyanskaya,et al.  Predicting effects of noncoding variants with deep learning–based sequence model , 2015, Nature Methods.

[7]  T. Andrews,et al.  Comparison of predicted and actual consequences of missense mutations , 2015, Proceedings of the National Academy of Sciences.

[8]  Benjamin J. Strober,et al.  A method to predict the impact of regulatory variants from DNA sequence , 2015, Nature Genetics.

[9]  Bin Yan,et al.  Exploring the function of genetic variants in the non-coding genomic regions: approaches for identifying human regulatory variants affecting gene expression , 2015, Briefings Bioinform..

[10]  Rémy Bruggmann,et al.  New insights into the performance of human whole-exome capture platforms , 2015, Nucleic acids research.

[11]  Xiaohui Xie,et al.  DANN: a deep learning approach for annotating the pathogenicity of genetic variants , 2015, Bioinform..

[12]  Michael Q. Zhang,et al.  Integrative analysis of 111 reference human epigenomes , 2015, Nature.

[13]  Rui Jiang,et al.  Pinpointing disease genes through phenomic and genomic data fusion , 2015, BMC Genomics.

[14]  Colin Campbell,et al.  An integrative approach to predicting the functional effects of non-coding and coding sequence variation , 2015, Bioinform..

[15]  Chongde Lin,et al.  The GABRB1 gene is associated with thalamus volume and modulates the association between thalamus volume and intelligence , 2014, NeuroImage.

[16]  P. Ng,et al.  Phen-Gen: combining phenotype and genotype to analyze rare disorders , 2014, Nature Methods.

[17]  Rui Jiang,et al.  Integrating Multiple Genomic Data to Predict Disease-Causing Nonsynonymous Single Nucleotide Variants in Exome Sequencing Studies , 2014, PLoS genetics.

[18]  J. Shendure,et al.  A general framework for estimating the relative pathogenicity of human genetic variants , 2014, Nature Genetics.

[19]  Damian Smedley,et al.  Improved exome prioritization of disease genes through cross-species phenotype comparison , 2014, Genome research.

[20]  Deanna M. Church,et al.  ClinVar: public archive of relationships among sequence variation and human phenotype , 2013, Nucleic Acids Res..

[21]  Damian Smedley,et al.  The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data , 2014, Nucleic Acids Res..

[22]  Gabor T. Marth,et al.  Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics , 2013, Science.

[23]  Bart De Moor,et al.  eXtasy: variant prioritization by genomic data fusion , 2013, Nature Methods.

[24]  Naomichi Matsumoto,et al.  De Novo mutations in GNAO1, encoding a Gαo subunit of heterotrimeric G proteins, cause epileptic encephalopathy. , 2013, American journal of human genetics.

[25]  Michael R. Johnson,et al.  De novo mutations in the classic epileptic encephalopathies , 2013, Nature.

[26]  Miguel Melo,et al.  Frequency of TERT promoter mutations in human cancers , 2013, Nature Communications.

[27]  Ting Chen,et al.  Exploring functional variant discovery in non-coding regions with SInBaD , 2012, Nucleic acids research.

[28]  De novo mutations in epileptic encephalopathies , 2013 .

[29]  Data production leads,et al.  An integrated encyclopedia of DNA elements in the human genome , 2012 .

[30]  ENCODEConsortium,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[31]  Adam Kiezun,et al.  Exome sequencing and the genetic basis of complex traits , 2012, Nature Genetics.

[32]  Evan T. Geller,et al.  Patterns and rates of exonic de novo mutations in autism spectrum disorders , 2012, Nature.

[33]  Rui Jiang,et al.  Constructing a gene semantic similarity network for the inference of disease genes , 2011, BMC Systems Biology.

[34]  Zhengyan Kan,et al.  Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer , 2011, Nature Genetics.

[35]  J. Shendure,et al.  Exome sequencing as a tool for Mendelian disease gene discovery , 2011, Nature Reviews Genetics.

[36]  Hui Jiang,et al.  Comprehensive comparison of three commercial human whole-exome capture platforms , 2011, Genome Biology.

[37]  J. Shendure,et al.  Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data , 2011, Nature Reviews Genetics.

[38]  C. Sander,et al.  Predicting the functional impact of protein mutations: application to cancer genomics , 2011, Nucleic acids research.

[39]  A. Gonzalez-Perez,et al.  Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel. , 2011, American journal of human genetics.

[40]  Serafim Batzoglou,et al.  Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++ , 2010, PLoS Comput. Biol..

[41]  H. Hakonarson,et al.  ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data , 2010, Nucleic acids research.

[42]  P. Bork,et al.  A method and server for predicting damaging missense mutations , 2010, Nature Methods.

[43]  James J. Yang.  Distribution of Fisher's combination statistic when the tests are dependent , 2010 .

[44]  L. Holm,et al.  The Pfam protein families database , 2005, Nucleic Acids Res..

[45]  Justin C. Fay,et al.  Identification of deleterious mutations within three human genomes. , 2009, Genome research.

[46]  Xiaohui Xie,et al.  Identifying novel constrained elements by exploiting biased substitution patterns , 2009, Bioinform..

[47]  S. Henikoff,et al.  Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm , 2009, Nature Protocols.

[48]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[49]  Michael Q. Zhang,et al.  Network-based global inference of human disease genes , 2008, Molecular systems biology.

[50]  Doron Betel,et al.  The microRNA.org resource: targets and expression , 2007, Nucleic Acids Res..

[51]  Simo V. Zhang,et al.  A map of human cancer signaling , 2007, Molecular systems biology.

[52]  C.-C. Jay Kuo,et al.  Sequence-based prioritization of nonsynonymous single-nucleotide polymorphisms for the study of disease mutations. , 2007, American journal of human genetics.

[53]  Bassem A. Hassan,et al.  Gene prioritization through genomic data fusion , 2006, Nature Biotechnology.

[54]  D. Haussler,et al.  Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. , 2005, Genome research.

[55]  S. Batzoglou,et al.  Distribution and intensity of constraint in mammalian genomic sequence. , 2005, Genome research.

[56]  S. Batalov,et al.  A gene atlas of the mouse and human protein-encoding transcriptomes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[57]  Cathy H. Wu,et al.  UniProt: the Universal Protein knowledgebase , 2004, Nucleic Acids Res..

[58]  John D. Storey.  The positive false discovery rate: a Bayesian interpretation and the q-value , 2003 .

[59]  P. Stenson,et al.  Human Gene Mutation Database (HGMD®): 2003 update , 2003, Human mutation.

[60]  Alexander E. Kel,et al.  TRANSFAC®: transcriptional regulation, from patterns to profiles , 2003, Nucleic Acids Res..

[61]  Maria Jesus Martin,et al.  The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003 , 2003, Nucleic Acids Res..

[62]  M. Daly,et al.  Guilt by association , 2000, Nature Genetics.

[63]  C E Lipscomb,et al.  Medical Subject Headings (MeSH). , 2000, Bulletin of the Medical Library Association.

[64]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[65]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[66]  D. Lindberg,et al.  The Unified Medical Language System , 1993, Yearbook of Medical Informatics.